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- PDB-10lp: Crystal structure of mouse CD38 with compound 9 -

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Basic information

Entry
Database: PDB / ID: 10lp
TitleCrystal structure of mouse CD38 with compound 9
ComponentsADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
KeywordsHYDROLASE / Inhibitor
Function / homology
Function and homology information


Nicotinate metabolism / phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / hydrolase activity, acting on glycosyl bonds / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide / long-term synaptic depression ...Nicotinate metabolism / phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / hydrolase activity, acting on glycosyl bonds / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide / long-term synaptic depression / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to hormone / B cell receptor signaling pathway / T cell activation / negative regulation of neuron projection development / positive regulation of insulin secretion / positive regulation of cell growth / signaling receptor activity / nuclear membrane / positive regulation of cytosolic calcium ion concentration / response to hypoxia / basolateral plasma membrane / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / membrane / identical protein binding / plasma membrane
Similarity search - Function
ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase
Similarity search - Domain/homology
: / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBrosey, C.A. / Bigelow, L. / Chapman, A. / Afanador, G. / Hodges, T.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Design and Exploration of a Tricyclic Series of CNS-Penetrant CD38 Small Molecule Inhibitors
Authors: Hodges, T.R. / Jang, Y. / Korch, K. / Osuma, A. / Randolph, J.T. / Shiroodi, R. / Bergstrom, B.D. / Brosey, C. / Jejurkar, P. / Sheehan, M.M. / Sadowski, R.N. / Lin, K.A. / Brown, J.W. / ...Authors: Hodges, T.R. / Jang, Y. / Korch, K. / Osuma, A. / Randolph, J.T. / Shiroodi, R. / Bergstrom, B.D. / Brosey, C. / Jejurkar, P. / Sheehan, M.M. / Sadowski, R.N. / Lin, K.A. / Brown, J.W. / Balakrishnan, A. / Zoi, I. / Bigelow, L. / Jain, R. / Bradley, N.P. / Chapman, A. / Korepanova, A. / Swensen, A.M. / Benekareddy, M. / Shotwell, J.B.
History
DepositionJan 27, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1002
Polymers30,2001
Non-polymers9011
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.585, 57.260, 58.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / 2'-phospho-cyclic-ADP-ribose transferase / ADP-ribosyl cyclase 1 / ADPRC 1 / Cyclic ADP-ribose hydrolase 1 / cADPR hydrolase 1 / I-19 / NIM-R5 antigen


Mass: 30199.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd38 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P56528, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#2: Chemical ChemComp-A1C6U / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[13-(1-cyclopropylsulfonylpyrazol-4-yl)-9-oxa-4$l^{4},6,12,14-tetrazatricyclo[8.4.0.0^{2,6}]tetradeca-1(14),2,4,10,12-pentaen-4-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 900.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H36N11O16P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350 and 200 mM ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.955→85.56 Å / Num. obs: 20996 / % possible obs: 98.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.19 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.069 / Rrim(I) all: 0.126 / Net I/σ(I): 12.2
Reflection shellResolution: 1.955→1.989 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2059 / CC1/2: 0.115 / CC star: 0.454 / Rpim(I) all: 1.826 / Rrim(I) all: 2.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→42.79 Å / SU ML: 0.2115 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2277 944 4.51 %
Rwork0.1903 19979 -
obs0.192 20923 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.13 Å2
Refinement stepCycle: LAST / Resolution: 1.96→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 60 213 2216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01282078
X-RAY DIFFRACTIONf_angle_d1.09362840
X-RAY DIFFRACTIONf_chiral_restr0.0665309
X-RAY DIFFRACTIONf_plane_restr0.0087365
X-RAY DIFFRACTIONf_dihedral_angle_d12.6949786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.060.28851480.21482790X-RAY DIFFRACTION98.36
2.06-2.190.30061220.21682734X-RAY DIFFRACTION95.45
2.19-2.360.27651060.20742809X-RAY DIFFRACTION96.84
2.36-2.590.23191330.19212863X-RAY DIFFRACTION99.57
2.59-2.970.23851240.19722873X-RAY DIFFRACTION98.68
2.97-3.740.21981650.17542871X-RAY DIFFRACTION99.12
3.74-42.790.19391460.1823039X-RAY DIFFRACTION98.67

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